Unearthing Neanderthal Population History Using Ancient Nuclear DNA From Cave Sediments

A new method extracts nuclear DNA from sediments, uncovering Neanderthal population shifts and opening broader possibilities for paleo-genetic research.

Mitochondrial DNA of archaic humans has been retrieved from cave sediments, but it has limited value for studying population relationships. Now, researchers present a method for analyzing trace amounts of archaic human nuclear DNA from sediments; their work studying ancient sediments from western Europe and southern Siberia has revealed new insights into Neanderthal population history.

While recent studies have shown that it’s possible to recover hominin mitochondrial DNA (mtDNA) from Pleistocene-age archaeological sediments, mtDNA only carries information about maternal lineage, which does not always reflect the complete genetic history of archaic humans. Although nuclear DNA contains far more information, its retrieval from sediments presents substantial challenges; it’s far less abundant than mtDNA and difficult to distinguish from other non-hominin mammalian and microbial DNA, which dominates the genetic material often present in ancient sediments.

To address these challenges, Benjamin Vernot and colleagues developed methods to recover, enrich, and analyze nuclear DNA from cave sediments. Specifically, Vernot et al. applied their approach to archaeological cave deposits from paleolithic sites in western Europe and southern Siberia dated to roughly 200,000 and 50,000 years ago.

Not only were the authors able to identify hominin nuclear DNA sequences in the Pleistocene sediments, but their analysis also revealed new insights into archaic human population history.

The findings suggest a Neanderthal population replacement event in northern Spain about 100,000 years ago, as well as two distinct Neanderthal radiation events during the early part of the Late Pleistocene that may have been associated with changing climate and environmental conditions. Their approach has the potential to substantially expand the settings in which hominin DNA can be recovered, the authors say.

Read Nuclear DNA From Cave Sediments Helps Unlock Ancient Human History for more on this research.

Reference: “Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments” by Benjamin Vernot, Elena I. Zavala, Asier Gómez-Olivencia, Zenobia Jacobs, Viviane Slon, Fabrizio Mafessoni, Frédéric Romagné, Alice Pearson, Martin Petr, Nohemi Sala, Adrián Pablos, Arantza Aranburu, José María Bermúdez de Castro, Eudald Carbonell, Bo Li, Maciej T. Krajcarz, Andrey I. Krivoshapkin, Kseniya A. Kolobova, Maxim B. Kozlikin, Michael V. Shunkov, Anatoly P. Derevianko, Bence Viola, Steffi Grote, Elena Essel, David López Herráez, Sarah Nagel, Birgit Nickel, Julia Richter, Anna Schmidt, Benjamin Peter, Janet Kelso, Richard G. Roberts, Juan-Luis Arsuaga and Matthias Meyer, 15 April 2021, Science.
DOI: 10.1126/science.abf1667

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